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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-02-13, 10:15 PST based on data in: /common/weinera2lab/UCLA/PSMA/WTS/QC_reports/FastQC

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        General Statistics

        Showing 140/140 rows and 3/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        Tu01-SSU-17-01578_S1_L006_R1_001
        39.1%
        48.0%
        150bp
        150bp
        18%
        52.4M
        Tu01-SSU-17-01578_S1_L006_R2_001
        37.5%
        48.0%
        150bp
        150bp
        36%
        52.4M
        Tu02-SSU-17-05920_S2_L006_R1_001
        72.1%
        49.0%
        150bp
        150bp
        36%
        39.9M
        Tu02-SSU-17-05920_S2_L006_R2_001
        71.3%
        50.0%
        150bp
        150bp
        55%
        39.9M
        Tu03-SSW-17-19048_S3_L006_R1_001
        49.1%
        49.0%
        150bp
        150bp
        18%
        43.7M
        Tu03-SSW-17-19048_S3_L006_R2_001
        47.9%
        50.0%
        150bp
        150bp
        36%
        43.7M
        Tu04-SSW-17-25773_S4_L006_R1_001
        50.6%
        46.0%
        150bp
        150bp
        27%
        38.2M
        Tu04-SSW-17-25773_S4_L006_R2_001
        49.2%
        46.0%
        150bp
        150bp
        18%
        38.2M
        Tu05-SSW-17-26286_S6_L006_R1_001
        46.3%
        47.0%
        150bp
        150bp
        27%
        42.8M
        Tu05-SSW-17-26286_S6_L006_R2_001
        45.2%
        48.0%
        150bp
        150bp
        27%
        42.8M
        Tu06-SSW-18-03623_S9_L006_R1_001
        94.8%
        50.0%
        150bp
        150bp
        36%
        28.3M
        Tu06-SSW-18-03623_S9_L006_R2_001
        93.7%
        51.0%
        150bp
        150bp
        27%
        28.3M
        Tu07-SSU-17-12780_S5_L006_R1_001
        91.1%
        53.0%
        150bp
        150bp
        36%
        37.6M
        Tu07-SSU-17-12780_S5_L006_R2_001
        90.0%
        54.0%
        150bp
        150bp
        36%
        37.6M
        Tu08-SSU-18-01790_S8_L006_R1_001
        79.0%
        51.0%
        150bp
        150bp
        27%
        39.4M
        Tu08-SSU-18-01790_S8_L006_R2_001
        78.1%
        52.0%
        150bp
        150bp
        55%
        39.4M
        Tu09-SSW-18-00437_S7_L006_R1_001
        72.2%
        56.0%
        150bp
        150bp
        45%
        41.6M
        Tu09-SSW-18-00437_S7_L006_R2_001
        70.9%
        57.0%
        150bp
        150bp
        55%
        41.6M
        Tu10-SSW-18-09187_S11_L006_R1_001
        97.7%
        54.0%
        150bp
        150bp
        27%
        29.8M
        Tu10-SSW-18-09187_S11_L006_R2_001
        96.6%
        54.0%
        150bp
        150bp
        36%
        29.8M
        Tu11-SSW-18-08336_S10_L006_R1_001
        97.0%
        53.0%
        150bp
        150bp
        36%
        30.2M
        Tu11-SSW-18-08336_S10_L006_R2_001
        96.0%
        54.0%
        150bp
        150bp
        27%
        30.2M
        Tu12-SSW-18-15123_S12_L006_R1_001
        36.4%
        48.0%
        150bp
        150bp
        45%
        43.7M
        Tu12-SSW-18-15123_S12_L006_R2_001
        34.8%
        49.0%
        150bp
        150bp
        45%
        43.7M
        Tu13-SSW-18-15123_S13_L006_R1_001
        53.0%
        50.0%
        150bp
        150bp
        45%
        45.9M
        Tu13-SSW-18-15123_S13_L006_R2_001
        51.6%
        51.0%
        150bp
        150bp
        55%
        45.9M
        Tu14-SSW-18-15123_S14_L006_R1_001
        62.6%
        52.0%
        150bp
        150bp
        45%
        44.3M
        Tu14-SSW-18-15123_S14_L006_R2_001
        61.5%
        55.0%
        150bp
        150bp
        55%
        44.3M
        Tu15-SSW-18-21924_S20_L006_R1_001
        48.6%
        50.0%
        150bp
        150bp
        18%
        43.9M
        Tu15-SSW-18-21924_S20_L006_R2_001
        47.3%
        50.0%
        150bp
        150bp
        36%
        43.9M
        Tu16-SSU-18-09500_S15_L006_R1_001
        41.0%
        45.0%
        150bp
        150bp
        18%
        49.2M
        Tu16-SSU-18-09500_S15_L006_R2_001
        39.5%
        46.0%
        150bp
        150bp
        18%
        49.2M
        Tu17-SSU-18-09917_S16_L006_R1_001
        72.8%
        51.0%
        150bp
        150bp
        36%
        42.9M
        Tu17-SSU-18-09917_S16_L006_R2_001
        71.9%
        53.0%
        150bp
        150bp
        55%
        42.9M
        Tu18-SSW-18-21177_S17_L006_R1_001
        91.3%
        63.0%
        150bp
        150bp
        27%
        38.5M
        Tu18-SSW-18-21177_S17_L006_R2_001
        89.5%
        63.0%
        150bp
        150bp
        27%
        38.5M
        Tu19-SSW-18-21177_S18_L006_R1_001
        92.9%
        52.0%
        150bp
        150bp
        27%
        38.5M
        Tu19-SSW-18-21177_S18_L006_R2_001
        92.0%
        52.0%
        150bp
        150bp
        36%
        38.5M
        Tu20-SSW-18-21972_S19_L006_R1_001
        38.9%
        49.0%
        150bp
        150bp
        18%
        43.6M
        Tu20-SSW-18-21972_S19_L006_R2_001
        37.7%
        50.0%
        150bp
        150bp
        27%
        43.6M
        Tu21-SSW-18-25614_S24_L006_R1_001
        76.3%
        61.0%
        150bp
        150bp
        36%
        40.2M
        Tu21-SSW-18-25614_S24_L006_R2_001
        74.7%
        61.0%
        150bp
        150bp
        45%
        40.2M
        Tu22-SSW-18-25614_S25_L006_R1_001
        84.6%
        54.0%
        150bp
        150bp
        27%
        37.5M
        Tu22-SSW-18-25614_S25_L006_R2_001
        83.5%
        54.0%
        150bp
        150bp
        27%
        37.5M
        Tu23-SSW-18-26865_S26_L006_R1_001
        58.9%
        45.0%
        150bp
        150bp
        27%
        44.3M
        Tu23-SSW-18-26865_S26_L006_R2_001
        57.6%
        46.0%
        150bp
        150bp
        27%
        44.3M
        Tu24-SSW-19-03158_S28_L006_R1_001
        50.2%
        48.0%
        150bp
        150bp
        27%
        40.8M
        Tu24-SSW-19-03158_S28_L006_R2_001
        48.8%
        49.0%
        150bp
        150bp
        18%
        40.8M
        Tu25-SSW-19-08792_S32_L006_R1_001
        70.5%
        52.0%
        150bp
        150bp
        36%
        44.4M
        Tu25-SSW-19-08792_S32_L006_R2_001
        69.8%
        53.0%
        150bp
        150bp
        55%
        44.4M
        Tu26-SSW-19-08792_S33_L006_R2_001
        33.1%
        48.0%
        150bp
        150bp
        27%
        46.9M
        Tu27-SSW-19-11127_S37_L006_R1_001
        74.7%
        50.0%
        150bp
        150bp
        36%
        40.3M
        Tu27-SSW-19-11127_S37_L006_R2_001
        73.9%
        51.0%
        150bp
        150bp
        45%
        40.3M
        Tu28-SSW-19-08679_S30_L006_R1_001
        63.6%
        46.0%
        150bp
        150bp
        27%
        36.7M
        Tu28-SSW-19-08679_S30_L006_R2_001
        62.3%
        47.0%
        150bp
        150bp
        36%
        36.7M
        Tu29-SSW-19-08679_S31_L006_R1_001
        55.1%
        52.0%
        150bp
        150bp
        45%
        45.1M
        Tu29-SSW-19-08679_S31_L006_R2_001
        53.5%
        52.0%
        150bp
        150bp
        45%
        45.1M
        Tu30-SSW-19-11106_S35_L006_R1_001
        62.9%
        48.0%
        150bp
        150bp
        36%
        42.7M
        Tu30-SSW-19-11106_S35_L006_R2_001
        61.8%
        49.0%
        150bp
        150bp
        36%
        42.7M
        Tu31-SSW-19-11106_S36_L006_R1_001
        77.3%
        54.0%
        150bp
        150bp
        36%
        41.4M
        Tu31-SSW-19-11106_S36_L006_R2_001
        76.3%
        54.0%
        150bp
        150bp
        55%
        41.4M
        Tu32-SSW-19-16434_S38_L006_R1_001
        87.5%
        50.0%
        150bp
        150bp
        27%
        21.9M
        Tu32-SSW-19-16434_S38_L006_R2_001
        86.4%
        51.0%
        150bp
        150bp
        27%
        21.9M
        Tu33-SSW-19-20545_S40_L006_R1_001
        42.6%
        47.0%
        150bp
        150bp
        18%
        46.8M
        Tu33-SSW-19-20545_S40_L006_R2_001
        41.7%
        48.0%
        150bp
        150bp
        27%
        46.8M
        Tu34-SSW-19-17421_S39_L006_R1_001
        58.5%
        52.0%
        150bp
        150bp
        36%
        44.6M
        Tu34-SSW-19-17421_S39_L006_R2_001
        57.7%
        53.0%
        150bp
        150bp
        45%
        44.6M
        Tu35-SSW-19-20955_S41_L006_R1_001
        89.6%
        59.0%
        150bp
        150bp
        45%
        6.5M
        Tu35-SSW-19-20955_S41_L006_R2_001
        87.6%
        60.0%
        150bp
        150bp
        45%
        6.5M
        Tu36-SSW-18-23322_S21_L006_R1_001
        95.9%
        53.0%
        150bp
        150bp
        36%
        30.0M
        Tu36-SSW-18-23322_S21_L006_R2_001
        94.8%
        54.0%
        150bp
        150bp
        45%
        30.0M
        Tu37-SSW-18-23322_S22_L006_R1_001
        70.2%
        45.0%
        150bp
        150bp
        27%
        41.5M
        Tu37-SSW-18-23322_S22_L006_R2_001
        69.1%
        46.0%
        150bp
        150bp
        27%
        41.5M
        Tu38-SSW-18-23322_S23_L006_R1_001
        81.3%
        52.0%
        150bp
        150bp
        36%
        39.5M
        Tu38-SSW-18-23322_S23_L006_R2_001
        80.5%
        52.0%
        150bp
        150bp
        55%
        39.5M
        Tu39-SSW-18-28062_S27_L006_R1_001
        86.2%
        51.0%
        150bp
        150bp
        36%
        43.4M
        Tu39-SSW-18-28062_S27_L006_R2_001
        85.5%
        51.0%
        150bp
        150bp
        45%
        43.4M
        Tu40-SSW-19-03362_S29_L006_R1_001
        91.4%
        63.0%
        150bp
        150bp
        36%
        30.4M
        Tu40-SSW-19-03362_S29_L006_R2_001
        89.3%
        64.0%
        150bp
        150bp
        36%
        30.4M
        Tu41-SSW-19-09322_S34_L006_R1_001
        54.5%
        50.0%
        150bp
        150bp
        36%
        46.8M
        Tu41-SSW-19-09322_S34_L006_R2_001
        53.8%
        51.0%
        150bp
        150bp
        45%
        46.8M
        Tu42-SSW-20-02006_S42_L006_R1_001
        47.8%
        50.0%
        150bp
        150bp
        27%
        46.6M
        Tu42-SSW-20-02006_S42_L006_R2_001
        46.8%
        51.0%
        150bp
        150bp
        45%
        46.6M
        Tu43-SSW-21-08161_S56_L006_R1_001
        85.4%
        50.0%
        150bp
        150bp
        45%
        2.7M
        Tu43-SSW-21-08161_S56_L006_R2_001
        85.0%
        54.0%
        150bp
        150bp
        55%
        2.7M
        Tu44-SSW-20-25251_S48_L006_R1_001
        39.6%
        49.0%
        150bp
        150bp
        27%
        42.6M
        Tu44-SSW-20-25251_S48_L006_R2_001
        38.6%
        49.0%
        150bp
        150bp
        45%
        42.6M
        Tu45-SSW-20-25251_S49_L006_R1_001
        86.3%
        58.0%
        150bp
        150bp
        36%
        21.5M
        Tu45-SSW-20-25251_S49_L006_R2_001
        84.5%
        59.0%
        150bp
        150bp
        45%
        21.5M
        Tu46-SSW-21-00440_S43_L006_R1_001
        83.5%
        49.0%
        150bp
        150bp
        27%
        33.8M
        Tu46-SSW-21-00440_S43_L006_R2_001
        82.5%
        50.0%
        150bp
        150bp
        27%
        33.8M
        Tu47-SSW-20-16894_S45_L006_R1_001
        88.4%
        50.0%
        150bp
        150bp
        27%
        5.1M
        Tu47-SSW-20-16894_S45_L006_R2_001
        88.0%
        52.0%
        150bp
        150bp
        36%
        5.1M
        Tu48-SSW-20-19610_S46_L006_R1_001
        90.4%
        53.0%
        150bp
        150bp
        36%
        14.8M
        Tu48-SSW-20-19610_S46_L006_R2_001
        89.7%
        54.0%
        150bp
        150bp
        45%
        14.8M
        Tu49-SSW-20-22066_S51_L006_R1_001
        90.0%
        61.0%
        150bp
        150bp
        45%
        18.7M
        Tu49-SSW-20-22066_S51_L006_R2_001
        88.5%
        62.0%
        150bp
        150bp
        45%
        18.7M
        Tu50-SSW-21-02477_S65_L006_R1_001
        93.8%
        49.0%
        150bp
        150bp
        27%
        10.5M
        Tu50-SSW-21-02477_S65_L006_R2_001
        92.8%
        50.0%
        150bp
        150bp
        36%
        10.5M
        Tu51-SSW-20-23191_S52_L006_R1_001
        82.5%
        62.0%
        150bp
        150bp
        55%
        0.5M
        Tu51-SSW-20-23191_S52_L006_R2_001
        81.7%
        72.0%
        150bp
        150bp
        55%
        0.5M
        Tu52-SSW-20-23950_S47_L006_R1_001
        55.0%
        44.0%
        150bp
        150bp
        36%
        32.7M
        Tu52-SSW-20-23950_S47_L006_R2_001
        53.4%
        45.0%
        150bp
        150bp
        45%
        32.7M
        Tu53-SSW-20-25415_S50_L006_R1_001
        86.0%
        50.0%
        150bp
        150bp
        27%
        36.8M
        Tu53-SSW-20-25415_S50_L006_R2_001
        85.4%
        51.0%
        150bp
        150bp
        36%
        36.8M
        Tu54-SSW-21-01930_S44_L006_R1_001
        89.9%
        68.0%
        150bp
        150bp
        45%
        11.5M
        Tu54-SSW-21-01930_S44_L006_R2_001
        86.7%
        69.0%
        150bp
        150bp
        55%
        11.5M
        Tu55-SSW-21-06354_S53_L006_R1_001
        85.6%
        49.0%
        150bp
        150bp
        36%
        4.9M
        Tu55-SSW-21-06354_S53_L006_R2_001
        84.9%
        50.0%
        150bp
        150bp
        36%
        4.9M
        Tu56-SSW-21-16454_S54_L006_R1_001
        40.0%
        46.0%
        150bp
        150bp
        18%
        48.3M
        Tu56-SSW-21-16454_S54_L006_R2_001
        37.7%
        46.0%
        150bp
        150bp
        27%
        48.3M
        Tu57-SSW-21-07964_S55_L006_R1_001
        43.3%
        44.0%
        150bp
        150bp
        18%
        48.6M
        Tu57-SSW-21-07964_S55_L006_R2_001
        40.5%
        44.0%
        150bp
        150bp
        18%
        48.6M
        Tu58-SSW-21-08904_S57_L006_R1_001
        62.9%
        52.0%
        150bp
        150bp
        27%
        39.2M
        Tu58-SSW-21-08904_S57_L006_R2_001
        61.6%
        52.0%
        150bp
        150bp
        45%
        39.2M
        Tu59-SSW-21-10938_S58_L006_R1_001
        38.3%
        47.0%
        150bp
        150bp
        18%
        55.6M
        Tu59-SSW-21-10938_S58_L006_R2_001
        37.1%
        48.0%
        150bp
        150bp
        27%
        55.6M
        Tu60-SSW-21-12058_S60_L006_R1_001
        66.1%
        47.0%
        150bp
        150bp
        36%
        41.6M
        Tu60-SSW-21-12058_S60_L006_R2_001
        65.2%
        48.0%
        150bp
        150bp
        36%
        41.6M
        Tu61-SSW-21-12058_S61_L006_R1_001
        57.0%
        46.0%
        150bp
        150bp
        36%
        42.5M
        Tu61-SSW-21-12058_S61_L006_R2_001
        55.9%
        47.0%
        150bp
        150bp
        36%
        42.5M
        Tu62-SSW-21-12160_S59_L006_R1_001
        93.3%
        54.0%
        150bp
        150bp
        36%
        30.9M
        Tu62-SSW-21-12160_S59_L006_R2_001
        92.4%
        54.0%
        150bp
        150bp
        36%
        30.9M
        Tu63-SSW-21-13334_S62_L006_R1_001
        53.7%
        48.0%
        150bp
        150bp
        27%
        43.7M
        Tu63-SSW-21-13334_S62_L006_R2_001
        52.5%
        48.0%
        150bp
        150bp
        45%
        43.7M
        Tu64-SSW-21-13334_S63_L006_R2_001
        45.4%
        49.0%
        150bp
        150bp
        27%
        39.0M
        Tu65-SSW-21-18824_S64_L006_R1_001
        89.8%
        45.0%
        150bp
        150bp
        27%
        13.3M
        Tu65-SSW-21-18824_S64_L006_R2_001
        89.4%
        46.0%
        150bp
        150bp
        27%
        13.3M
        Tu66-SSW-21-18967_S66_L006_R1_001
        89.6%
        53.0%
        150bp
        150bp
        36%
        35.1M
        Tu66-SSW-21-18967_S66_L006_R2_001
        88.6%
        53.0%
        150bp
        150bp
        36%
        35.1M
        Tu67-SSW-21-21772_S67_L006_R1_001
        43.2%
        45.0%
        150bp
        150bp
        18%
        42.8M
        Tu67-SSW-21-21772_S67_L006_R2_001
        42.2%
        46.0%
        150bp
        150bp
        27%
        42.8M
        Tu68-SSW-21-23514_S68_L006_R1_001
        84.1%
        46.0%
        150bp
        150bp
        36%
        34.3M
        Tu68-SSW-21-23514_S68_L006_R2_001
        83.5%
        46.0%
        150bp
        150bp
        36%
        34.3M
        Tu69-SSW-21-23548_S69_L006_R1_001
        52.5%
        48.0%
        150bp
        150bp
        27%
        41.2M
        Tu69-SSW-21-23548_S69_L006_R2_001
        51.4%
        49.0%
        150bp
        150bp
        36%
        41.2M
        Tu70-SSW-21-23650_S70_L006_R1_001
        36.7%
        44.0%
        150bp
        150bp
        18%
        52.5M
        Tu70-SSW-21-23650_S70_L006_R2_001
        35.2%
        45.0%
        150bp
        150bp
        27%
        52.5M
        Tu71-SSW-21-24145_S71_L006_R1_001
        91.2%
        56.0%
        150bp
        150bp
        45%
        35.4M
        Tu71-SSW-21-24145_S71_L006_R2_001
        88.9%
        57.0%
        150bp
        150bp
        45%
        35.4M

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        All samples have sequences of a single length (150bp)

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        71
        59196395
        1.1792%
        TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
        17
        1197425
        0.0239%
        AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        13
        1150006
        0.0229%
        GCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGG
        13
        800717
        0.0159%
        CAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAG
        12
        843446
        0.0168%
        CTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGT
        10
        551605
        0.0110%
        CTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCAT
        10
        567193
        0.0113%
        GTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAA
        8
        650012
        0.0129%
        CCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCAACCTGGTGGTCC
        8
        427850
        0.0085%
        CCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATG
        7
        413755
        0.0082%
        CCCCACCCCCGGCCCCGCCCGCCCACCCCCGCACCCGCCGGAGCCCGCCC
        7
        256869
        0.0051%
        AACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCCGACT
        6
        519009
        0.0103%
        CGGGAACGTATTCACCGCAGCGTTGCTGATCTGCGATTACTAGCGACTCC
        6
        479696
        0.0096%
        GGAGTATTTAGGCTTGACGGGTGGTCCCGCCAGATTCACGCGAAATTCCA
        6
        426157
        0.0085%
        CTGGAGTCTTGGAAGCTTGACTACCCTACGTTCTCCTACAAATGGACCTT
        6
        272552
        0.0054%
        CCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATAT
        6
        316926
        0.0063%
        CGGATTTTCAAGGGCCAGCGAGAGCTCACCGGACGCCGCCGGAACCGCGA
        6
        327135
        0.0065%
        CCCGGGGCTCCCGCCGGCTTCTCCGGGATCGGTCGCGTTACCGCACTGGA
        6
        306429
        0.0061%
        CCACCCCCGGCCCCGCCCGCCCACCCCCGCACCCGCCGGAGCCCGCCCCC
        6
        260683
        0.0052%
        CCCACCCCCGGCCCCGCCCGCCCACCCCCGCACCCGCCGGAGCCCGCCCC
        6
        228305
        0.0045%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1